rs11592052

Positions:

• chr10-32511838-G-A
• chr10-32511838-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001395015.1(CCDC7):​c.873-6107G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 748,288 control chromosomes in the GnomAD database, including 71,298 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.34 (11478 hom., cov: 33)
  • Exomes 𝑓: 0.43 (59820 hom.)
• Consequence: CCDC7 NM_001395015.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411

Genes affected

CCDC7 (HGNC:26533): (coiled-coil domain containing 7)

CCDC7 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC7	NM_001395015.1	c.873-6107G>A		intron_variant		ENST00000639629.2	NP_001381944.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC7	ENST00000639629.2	c.873-6107G>A		intron_variant		5	NM_001395015.1	ENSP00000491655.1

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52479 AN: 152078 Hom.: 11475 Cov.: 33

Gnomad AFR AF: 0.0951

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.0879

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.361

GnomAD4 exome AF: 0.431 AC: 256695 AN: 596092 Hom.: 59820 Cov.: 7 AF XY: 0.429 AC XY: 135260 AN XY: 314944

Gnomad4 AFR exome AF: 0.0928

Gnomad4 AMR exome AF: 0.355

Gnomad4 ASJ exome AF: 0.471

Gnomad4 EAS exome AF: 0.100

Gnomad4 SAS exome AF: 0.335

Gnomad4 FIN exome AF: 0.496

Gnomad4 NFE exome AF: 0.488

Gnomad4 OTH exome AF: 0.402

GnomAD4 genome AF: 0.345 AC: 52482 AN: 152196 Hom.: 11478 Cov.: 33 AF XY: 0.341 AC XY: 25408 AN XY: 74406

Gnomad4 AFR AF: 0.0948

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.0881

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.361

Alfa AF: 0.309 Hom.: 1205

Bravo AF: 0.322

Asia WGS AF: 0.193 AC: 671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.3
DANN	Benign	0.83

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11592052; hg19: chr10-32800766;